I want to quantitatively compare ChIP-seq data between different subtypes of a cancer.
My experimental design is as follows: I have multiple samples enriched for 3 different histone marks from 2 subtypes of a cancer and there are no replicates for them. The sample structure somewhat looks like this:
Subtype 1 Sample_A_K4me3, Sample_A_K27me3, Sample_A_K27ac, Sample_1_input, Sample_B_K4me3, Sample_B_K27me3, Sample_B_K27ac, Sample_2_input, Sample_C_K4me3, Sample_C_K27me3, Sample_C_K27ac and Sample_3_input Subtype 2 Sample_1_K4me3, Sample_1_K27me3, Sample_1_K27ac, Sample_1_input, Sample_2_K4me3, Sample_2_K27me3, Sample_2_K27ac, Sample_2_input, Sample_3_K4me3, Sample_3_K27me3, Sample_3_K27ac and Sample_3_input
Since, I am interested to call differential binding sites between the subtypes of a cancer, Can I use these samples (like samples A,B and C) which are enriched for same histone mark (say K4me3) from same subtype as a surrogate to replicates and compare it with the similar set (1,2 and 3) from other subtype?
If this is ok which tool is recommended to use in order to compare these unpaired samples and call differential binding sites between both the subtypes.
Thanks in advance.